Huaihe River basin was suffering from both the problems of water resources shortage and water quality-induced water shortage. The policies of contemporary eco-compensation in practic had unclear definition, regional limitations and also in lack of diversified compensation methods. In light of water contamination problem in Huaihe River basin, a new policy framework for eco-compensation was put forward based on water quality and quantity. Meanwhile, the analysis and exploration were carried on from the views of accounting, organization and compensation form. The results showed that the framework can fully reflect across different provinces, regions of the differences of water quality and quantity, compared with current ecological compensation pratices in Huaihe River basin, It was more preferable in operability, applicability and coverage.